I can't be of much help on the tools issue but the "Request-URI Too Large"
error can be fixed by adding a line like :
(the size is a number of bytes which reflects the length of the uri eventually. For my
setup, the above number does the job)
This line shall be added into your httpd.conf of ssl.conf in case you are using https
connection. It shall be placed within
<VirtualHost *: ... >
Nikolay Vazov, PhD
Department for Research Computing, University of Oslo
From: galaxy-dev <galaxy-dev-bounces(a)lists.galaxyproject.org> on behalf of Sarah
Sent: 20 July 2016 09:51
Subject: [galaxy-dev] errors when updating tools
I just updated our Galaxy from 15.10 to 16.04. I also wanted to update the tools
installed, but I'm (again) getting a whole bunch of different errors.
Some of the updated tools rely on package_cairo_1_12_14, which fails, because it cannot
find some of it's dependencies (see package_cairo_errors.jpg):
Error installing tool dependency fontconfig version 2.11.1: Unable to
locate required tool shed repository named package_fontconfig_2_11_1 owned by iuc with
Error installing tool dependency freetype version 2.5.2: Unable to locate required tool
shed repository named package_freetype_2_5_2 owned by iuc with revision 3b09e7916896.
In the main overview of the repository I also see the message "Dependency was not
resolved by any resolver module." (see package_cairo_resolver.jpg). Is this related
and something I should worry about? I did not touch the resolver configuration, I left the
line in galaxy.ini commented.
I also don't understand why it tries to install a different revision of a package repo
that's already installed. I'm having similar errors for some other packages.
Furthermore, when I try to "Get Updates" for cuffdiff, I get an internal server
error (see cuffdiff_update_error.txt). The same for macs2 (see macs2_update_error.jpg).
When I try to install the newest version of cuffdiff from the toolshed, after I click
"Install to Galaxy", I get a "Request-URI Too Large" error (from
apache I guess). The last message before it fails in the Galaxy log is "Building
repository dependency relationships...".
I'm a bit reluctant to update any package repositories I have installed, since in the
past this lead to dependencies breaking. Also uninstalling and reinstalling usually
doesn't help, since the database keeps the records and once it's messed up it
stays messed up. I checked on the galaxy-stable docker image and there everything works
fine, so I guess it's related to my Galaxy instance, not the package/tool
Any help on how to solve this is greatly appreciated!
HPC System Administrator
UNIVERSITÉ DU LUXEMBOURG
LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
T +352 46 66 44 5360
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